scholarly journals Bacterial Communities Associated with Human Decomposition

2021 ◽  
Author(s):  
◽  
Rachel Parkinson
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Interval Estimation ◽  
Molecular Profiling ◽  
Human Cadaver ◽  
Bacterial Populations ◽  
Human Decomposition ◽  
Microbial Biomarkers ◽  
Pig Carcasses ◽  
Bacterial Groups

<p>Human decomposition is a little-understood process with even less currently known about the microbiology involved. The aim of this research was to investigate the bacterial community associated with exposed decomposing mammalian carcasses on soil and to determine whether changes in this community could potentially be used to determine time since death in forensic investigations. A variety of soil chemistry and molecular biology methods, including molecular profiling tools T-RFLP and DGGE were used to explore how and when bacterial communities change during the course of a decomposition event. General bacterial populations and more specific bacterial groups were examined. Decomposition was shown to cause significant and sequential changes in the bacterial communities within the soil, and changes in the bacterial community often correlated with visual changes in the stage of decomposition. Organisms derived from the cadavers and carcasses were able to be detected, using molecular methods, in the underlying soil throughout the decomposition period studied. There was little correlation found between decomposition stage and the presence and diversity within the specific bacterial groups investigated. Organisms contributing to the changes seen in the bacterial communities using molecular profiling methods were identified using a cloning and sequencing based technique and included soil and environment-derived bacteria, as well as carcass or cadaver-derived organisms. This research demonstrated that pig (Sus scrofa) carcass and human cadaver decomposition result in similar bacterial community changes in soil, confirming that pig carcasses are a good model for studying the microbiology of human decomposition. The inability to control for differences between donated human cadavers made understanding the human cadaver results difficult, whereas pig carcass study allowed many variables to be held constant while others were investigated. The information gained from this study about the bacteria associated with a cadaver and how the community alters over the course of decomposition may, in the future, enable the development of a forensic post mortem interval estimation tool based on these changes in the bacterial community over time. The findings in this thesis suggest that high variability between human bodies and their microflora is likely to present a challenge to the development of such a tool, but further study with emerging high-throughput molecular tools may enable identification of microbial biomarkers for this purpose.</p>

scholarly journals Bacterial Communities Associated with Human Decomposition

2021 ◽  
Author(s):  
◽  
Rachel Parkinson
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Interval Estimation ◽  
Molecular Profiling ◽  
Human Cadaver ◽  
Bacterial Populations ◽  
Human Decomposition ◽  
Microbial Biomarkers ◽  
Pig Carcasses ◽  
Bacterial Groups

<p>Human decomposition is a little-understood process with even less currently known about the microbiology involved. The aim of this research was to investigate the bacterial community associated with exposed decomposing mammalian carcasses on soil and to determine whether changes in this community could potentially be used to determine time since death in forensic investigations. A variety of soil chemistry and molecular biology methods, including molecular profiling tools T-RFLP and DGGE were used to explore how and when bacterial communities change during the course of a decomposition event. General bacterial populations and more specific bacterial groups were examined. Decomposition was shown to cause significant and sequential changes in the bacterial communities within the soil, and changes in the bacterial community often correlated with visual changes in the stage of decomposition. Organisms derived from the cadavers and carcasses were able to be detected, using molecular methods, in the underlying soil throughout the decomposition period studied. There was little correlation found between decomposition stage and the presence and diversity within the specific bacterial groups investigated. Organisms contributing to the changes seen in the bacterial communities using molecular profiling methods were identified using a cloning and sequencing based technique and included soil and environment-derived bacteria, as well as carcass or cadaver-derived organisms. This research demonstrated that pig (Sus scrofa) carcass and human cadaver decomposition result in similar bacterial community changes in soil, confirming that pig carcasses are a good model for studying the microbiology of human decomposition. The inability to control for differences between donated human cadavers made understanding the human cadaver results difficult, whereas pig carcass study allowed many variables to be held constant while others were investigated. The information gained from this study about the bacteria associated with a cadaver and how the community alters over the course of decomposition may, in the future, enable the development of a forensic post mortem interval estimation tool based on these changes in the bacterial community over time. The findings in this thesis suggest that high variability between human bodies and their microflora is likely to present a challenge to the development of such a tool, but further study with emerging high-throughput molecular tools may enable identification of microbial biomarkers for this purpose.</p>

scholarly journals Soil Element Stoichiometry Drives Bacterial Community Composition Following Thinning in A Larix Plantation in the Subalpine Regions of Northern China

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 261
Author(s):  
Mengke Cai ◽  
Xinhao Peng ◽  
Xiaoqin Cheng ◽  
Li Liu ◽  
Shiping Xing ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
High Intensity ◽  
Bacterial Communities ◽  
Soil Resource ◽  
Low Intensity ◽  
Medium Intensity ◽  
Elemental Stoichiometry ◽  
Tree Removal ◽  
Bacterial Groups

It is well established that forest thinning alters aboveground plant community composition and soil resource availability. However, how it regulates the composition and diversity of belowground microbial communities remains unclear. To quantify the effects of thinning on soil bacterial groups and the underlying mechanisms of these effects, this research was conducted in a Larix principis-rupprechtii Mayr. plantation with various thinning intensities, including a control (0% tree removal), a low-intensity treatment (15% tree removal), a medium-intensity treatment (35% tree removal), and a high-intensity treatment (50% tree removal). Compared to the control, the medium and high intensity thinning treatments significantly improved soil moisture, nutrient concentrations (including soil total carbon, nitrogen, phosphorus, and ammonium nitrogen), microbial biomass, and elemental stoichiometry ratios. The abundance and diversity of bacterial communities peaked in the medium-intensity treatment. Thinning also had strong effects on dominant bacterial groups at the phylum level. For instance, Bacteroidetes and Nitrospirae were significantly increased in the medium-intensity treatment (MIT), while the Gemmatimonadetes were significantly decreased in the low-intensity treatment (LIT). Combining Spearman correlation analysis and redundancy analysis demonstrated that thinning could facilitate the assembly of unique bacterial communities, and these shifts in microorganisms could probably be attributed to corresponding changes in soil resource stoichiometry. In conclusion, this study provides novel evidence that rational thinning could promote belowground bacterial community diversity and that elemental stoichiometry is an important indicator in shaping forest soil bacterial communities.

scholarly journals Long-term continuously monocropped peanut significantly changed the abundance and composition of soil bacterial communities

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9024
Author(s):  
Mingna Chen ◽  
Hu Liu ◽  
Shanlin Yu ◽  
Mian Wang ◽  
Lijuan Pan ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Abundant Species ◽  
Bacterial Populations ◽  
Soil Sickness ◽  
Community Function ◽  
Soil Bacterial Communities ◽  
Short And Long Term

Soil sickness is the progressive loss of soil quality due to continuous monocropping. The bacterial populations are critical to sustaining agroecosystems, but their responses to long-term peanut monocropping have not been determined. In this study, based on a previously constructed gradient of continuous monocropped plots, we tracked the detailed feedback responses of soil bacteria to short- and long-term continuous monocropping of four different peanut varieties using high-throughput sequencing techniques. The analyses showed that soil samples from 1- and 2-year monocropped plots were grouped into one class, and samples from the 11- and 12-year plots were grouped into another. Long-term consecutive monocropping could lead to a general loss in bacterial diversity and remarkable changes in bacterial abundance and composition. At the genera level, the dominant genus Bacillus changed in average abundance from 1.49% in short-term monocropping libraries to 2.96% in the long-term libraries. The dominant species Bacillus aryabhattai and Bacillus funiculus and the relatively abundant species Bacillus luciferensis and Bacillus decolorationis all showed increased abundance with long-term monocropping. Additionally, several other taxa at the genus and species level also presented increased abundance with long-term peanut monocropping; however, several taxa showed decreased abundance. Comparing analyses of predicted bacterial community functions showed significant changes at different KEGG pathway levels with long-term peanut monocropping. Combined with our previous study, this study indicated that bacterial communities were obviously influenced by the monocropping period, but less influenced by peanut variety and growth stage. Some bacterial taxa with increased abundance have functions of promoting plant growth or degrading potential soil allelochemicals, and should be closely related with soil remediation and may have potential application to relieve peanut soil sickness. A decrease in diversity and abundance of bacterial communities, especially beneficial communities, and simplification of bacterial community function with long-term peanut monocropping could be the main cause of peanut soil sickness.

scholarly journals Epichloë Fungal Endophytes Influence Seed-Associated Bacterial Communities

2022 ◽  
Vol 12 ◽  
Author(s):  
Daniel A. Bastías ◽  
Ludmila Bubica Bustos ◽  
Ruy Jáuregui ◽  
Andrea Barrera ◽  
Ian S. Acuña-Rodríguez ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Lolium Multiflorum ◽  
Rhopalosiphum Padi ◽  
Fungal Endophytes ◽  
Insect Herbivores ◽  
Bacterial Microbiota ◽  
Mother Plants ◽  
Bacterial Groups

Seeds commonly harbour diverse bacterial communities that can enhance the fitness of future plants. The bacterial microbiota associated with mother plant’s foliar tissues is one of the main sources of bacteria for seeds. Therefore, any ecological factor influencing the mother plant’s microbiota may also affect the diversity of the seed’s bacterial community. Grasses form associations with beneficial vertically transmitted fungal endophytes of genus Epichloë. The interaction of plants with Epichloë endophytes and insect herbivores can influence the plant foliar microbiota. However, it is unknown whether these interactions (alone or in concert) can affect the assembly of bacterial communities in the produced seed. We subjected Lolium multiflorum plants with and without its common endophyte Epichloë occultans (E+, E-, respectively) to an herbivory treatment with Rhopalosiphum padi aphids and assessed the diversity and composition of the bacterial communities in the produced seed. The presence of Epichloë endophytes influenced the seed bacterial microbiota by increasing the diversity and affecting the composition of the communities. The relative abundances of the bacterial taxa were more similarly distributed in communities associated with E+ than E- seeds with the latter being dominated by just a few bacterial groups. Contrary to our expectations, seed bacterial communities were not affected by the aphid herbivory experienced by mother plants. We speculate that the enhanced seed/seedling performance documented for Epichloë-host associations may be explained, at least in part, by the Epichloë-mediated increment in the seed-bacterial diversity, and that this phenomenon may be applicable to other plant-endophyte associations.

scholarly journals Geographic and Host-Associated Variations in Bacterial Communities on the Floret Surfaces of Field-Grown Broccoli

2018 ◽  
Vol 84 (8) ◽  
pp. e02837-17 ◽  
Author(s):  
Min-Soo Kim ◽  
Jin-Woo Bae ◽  
Eun-Jin Park
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Associated Factors ◽  
Bacterial Community Composition ◽  
Leafy Vegetables ◽  
Bacterial Populations ◽  
Content Type ◽  
Fresh Vegetables ◽  
Tree Fruits

ABSTRACT Fresh vegetables harbor diverse bacterial populations on their surfaces. However, information on this microbiota is limited to a few types of fresh vegetables, and little is known about how it varies with geography and host condition. Here, we analyzed bacterial communities on the floret surfaces of 66 field-grown broccoli collected from 22 farms in four farming regions of Jeju Island, South Korea, using 454 pyrosequencing of 16S rRNA amplicons, and we determined their relationships to farming region and host-associated factors. Geographic variations in bacterial community composition and diversity were observed among farming regions, which partly reflected their relative humidity and insolation. The most abundant phyla were Proteobacteria, followed by Actinobacteria, Firmicutes, and Bacteroidetes; core operational taxonomic units (OTUs) assigned to Pseudomonas, Acinetobacter, Oxalobacteraceae, Comamonadaceae, and Enterobacteriaceae contributed to the community differences. Bacterial community composition differed between immature and mature samples, with mature samples harboring higher bacterial diversity. In comparison with communities on other types of fresh vegetables and fruits, bacterial communities on broccoli florets were unique but more similar to those of ground vegetables than to those of tree fruits/vegetables. This study presents novel data on the variability of floret-associated bacterial populations of field-grown broccoli relative to environmental and host-associated factors.IMPORTANCE Fresh vegetables harbor diverse and complex bacterial populations on their surfaces. These indigenous bacteria may play a role in human and crop health; however, the diversity and variability of bacterial communities on fresh vegetables require further study. A popular crop of leafy vegetables, broccoli, is of great agricultural and industrial importance. This study provides a detailed description of the bacterial community composition and diversity on the surfaces of broccoli florets. The variability of bacterial communities is associated with the geographic location of farming sites and is affected by host growth and health. The bacterial communities specific to broccoli were identified and showed greater similarity to those found on ground vegetables than to those found on tree fruits/vegetables. This study presents novel data on the impact of environmental and host-associated conditions on the variability of floret-associated bacterial populations present on field-grown broccoli.

scholarly journals Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3075 ◽  
Author(s):  
Sheila Torres ◽  
Jonathan B. Clayton ◽  
Jessica L. Danzeisen ◽  
Tonya Ward ◽  
Hu Huang ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Skin Microbiome ◽  
Bacterial Populations ◽  
Operational Taxonomic Units ◽  
Hair Type ◽  
Different Seasons ◽  
Over Time

It has previously been shown that domestic dogs and their household owners share bacterial populations, and that sharing of bacteria between humans is facilitated through the presence of dogs in the household. However, less is known regarding the bacterial communities of dogs, how these communities vary by location and over time, and how cohabitation of dogs themselves influences their bacterial community. Furthermore, the effects of factors such as breed, hair coat length, sex, shedding, and age on the canine skin microbiome is unknown. This study sampled the skin bacterial communities of 40 dogs belonging to 20 households longitudinally across three seasons (spring, summer, and winter). Significant differences in bacterial community structure between samples were identified when stratified by season, but not by dog sex, age, breed, hair type, or skin site. Cohabitating dogs were more likely to share bacteria of the skin than non-cohabitating dogs. Similar to human bacterial microbiomes, dogs’ microbiomes were more similar to their own microbiomes over time than to microbiomes of other individuals. Dogs sampled during the same season were also more similar to each other than to dogs from different seasons, irrespective of household. However, there were very few core operational taxonomic units (OTUs) identified across all dogs sampled. Taxonomic classification revealedPropionibacterium acnesandHaemophilussp. as key members of the dog skin bacterial community, along withCorynebacteriumsp. andStaphylococcus epidermidis. This study shows that the skin bacterial community structure of dogs is highly individualized, but can be shared among dogs through cohabitation.

scholarly journals Habitats Are More Important Than Seasons in Shaping Soil Bacterial Communities on the Qinghai-Tibetan Plateau

2021 ◽  
Vol 9 (8) ◽  
pp. 1595
Author(s):  
Rui Wang ◽  
Miao Wang ◽  
Jing Wang ◽  
Yinghua Lin
Keyword(s):  
Tibetan Plateau ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Seasonal Changes ◽  
Relative Effect ◽  
Soil Bacterial Communities ◽  
Bacterial Dynamics ◽  
Composition And Structure ◽  
Microbial Biomarkers ◽  
Soil Bacterial

Both habitats and seasons can determine the dynamics of microbial communities, but the relative importance of different habitats and seasonal changes in shaping the soil bacterial community structures on a small spatial scale in permafrost areas remains controversial. In this study, we explored the relative effect of four typical alpine meadow habitats (swamp wetland, swamp meadow, meadow and mature meadow) versus seasons on soil bacterial communities based on samples from the Qinghai-Tibetan Plateau in four months (March, May, July and September). The results showed that habitats, rather than seasons explained more variation of soil bacterial composition and structure. Environmental cofactors explained the greatest proportion of bacterial variation observed and can help elucidate the driving force of seasonal changes and habitats on bacterial communities. Soil temperature played the most important role in shaping bacterial beta diversities, followed by soil total nitrogen and pH. A group of microbial biomarkers, used as indicators of different months, were identified using random forest modeling, and for which relative abundance was shaped by different environmental factors. Furthermore, seasonality in bacterial co-occurrence patterns was observed. The data showed that co-occurrence relationships changed over months. The inter-taxa connections in May and July were more pronounced than that in March and September. Bryobacter, a genus of subgroup_22 affiliated to Acidobacteria, and Pseudonocardia belonging to Actinobacteria were observed as the keystone taxa in different months in the network. These results demonstrate that the bacterial community was clustered according to the seasonal mechanism, whereas the co-occurrence relationships changed over months, which indicated complex bacterial dynamics in a permafrost grassland on the eastern edge of Qinghai-Tibetan.

scholarly journals Bacterial community structure of early-stage biofilms is dictated by temporal succession rather than substrate types in the southern coastal seawater of India

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257961
Author(s):  
T. J. Sushmitha ◽  
Meora Rajeev ◽  
P. Sriyutha Murthy ◽  
S. Ganesh ◽  
Subba Rao Toleti ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Marine Environment ◽  
Bacterial Communities ◽  
Early Stage ◽  
Substrate Material ◽  
Community Succession ◽  
Temporal Succession ◽  
Biofilm Development ◽  
Bacterial Groups ◽  
Planktonic Community

Bacterial communities colonized on submerged substrata are recognized as a key factor in the formation of complex biofouling phenomenon in the marine environment. Despite massive maritime activities and a large industrial sector in the nearshore of the Laccadive Sea, studies describing pioneer bacterial colonizers and community succession during the early-stage biofilm are scarce. We investigated the biofilm-forming bacterial community succession on three substrata viz. stainless steel, high-density polyethylene, and titanium over 15 days of immersion in the seawater intake area of a power plant, located in the southern coastal region of India. The bacterial community composition of biofilms and peripheral seawater were analyzed by Illumina MiSeq sequenced 16S rRNA gene amplicons. The obtained metataxonomic results indicated a profound influence of temporal succession over substrate type on the early-stage biofilm-forming microbiota. Bacterial communities showed vivid temporal dynamics that involved variations in abundant bacterial groups. The proportion of dominant phyla viz. Proteobacteria decreased over biofilm succession days, while Bacteroidetes increased, suggesting their role as initial and late colonizers, respectively. A rapid fluctuation in the proportion of two bacterial orders viz. Alteromonadales and Vibrionales were observed throughout the successional stages. LEfSe analysis identified specific bacterial groups at all stages of biofilm development, whereas no substrata type-specific groups were observed. Furthermore, the results of PCoA and UPGMA hierarchical clustering demonstrated that the biofilm-forming community varied considerably from the planktonic community. Phylum Proteobacteria preponderated the biofilm-forming community, while the Bacteroidetes, Cyanobacteria, and Actinobacteria dominated the planktonic community. Overall, our results refute the common assumption that substrate material has a decisive impact on biofilm formation; rather, it portrayed that the temporal succession overshadowed the influence of the substrate material. Our findings provide a scientific understanding of the factors shaping initial biofilm development in the marine environment and will help in designing efficient site-specific anti-biofouling strategies.

scholarly journals The capacity of wastewater treatment plants drives bacterial community structure and its assembly

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Young Kyung Kim ◽  
Keunje Yoo ◽  
Min Sung Kim ◽  
Il Han ◽  
Minjoo Lee ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Community Structure ◽  
Bacterial Community ◽  
Activated Sludge ◽  
Community Assembly ◽  
Bacterial Communities ◽  
Wastewater Treatment Plants ◽  
High Capacity ◽  
Operating Conditions ◽  
Rrna Gene

Abstract Bacterial communities in wastewater treatment plants (WWTPs) affect plant functionality through their role in the removal of pollutants from wastewater. Bacterial communities vary extensively based on plant operating conditions and influent characteristics. The capacity of WWTPs can also affect the bacterial community via variations in the organic or nutrient composition of the influent. Despite the importance considering capacity, the characteristics that control bacterial community assembly are largely unknown. In this study, we discovered that bacterial communities in WWTPs in Korea and Vietnam, which differ remarkably in capacity, exhibit unique structures and interactions that are governed mainly by the capacity of WWTPs. Bacterial communities were analysed using 16S rRNA gene sequencing and exhibited clear differences between the two regions, with these differences being most pronounced in activated sludge. We found that capacity contributed the most to bacterial interactions and community structure, whereas other factors had less impact. Co-occurrence network analysis showed that microorganisms from high-capacity WWTPs are more interrelated than those from low-capacity WWTPs, which corresponds to the tighter clustering of bacterial communities in Korea. These results will contribute to the understanding of bacterial community assembly in activated sludge processing.

scholarly journals Co-Occurrence of Regulated and Emerging Mycotoxins in Corn Silage: Relationships with Fermentation Quality and Bacterial Communities

Toxins ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 232
Author(s):  
Antonio Gallo ◽  
Francesca Ghilardelli ◽  
Alberto Stanislao Atzori ◽  
Severino Zara ◽  
Barbara Novak ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Dry Matter ◽  
Kojic Acid ◽  
Corn Silage ◽  
Fungal Metabolites ◽  
Fusarium Mycotoxins ◽  
Low Concentrations ◽  
Fermentation Quality ◽  
Low Levels

Sixty-four corn silages were characterized for chemicals, bacterial community, and concentrations of several fungal metabolites. Silages were grouped in five clusters, based on detected mycotoxins, and they were characterized for being contaminated by (1) low levels of Aspergillus- and Penicillium-mycotoxins; (2) low levels of fumonisins and other Fusarium-mycotoxins; (3) high levels of Aspergillus-mycotoxins; (4) high levels of non-regulated Fusarium-mycotoxins; (5) high levels of fumonisins and their metabolites. Altersetin was detected in clusters 1, 3, and 5. Rugulusovin or brevianamide F were detected in several samples, with the highest concentration in cluster 3. Emodin was detected in more than 50.0% of samples of clusters 1, 3 and 5, respectively. Kojic acid occurred mainly in clusters 1 and 2 at very low concentrations. Regarding Fusarium mycotoxins, high occurrences were observed for FB3, FB4, FA1, whereas the average concentrations of FB6 and FA2 were lower than 12.4 µg/kg dry matter. Emerging Fusarium-produced mycotoxins, such as siccanol, moniliformin, equisetin, epiequisetin and bikaverin were detected in the majority of analyzed corn silages. Pestalotin, oxaline, phenopirrozin and questiomycin A were detected at high incidences. Concluding, this work highlighted that corn silages could be contaminated by a high number of regulated and emerging mycotoxins.

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